Justin Lemkul jalemkul at vt.edu
Thu Aug 22 22:33:03 CEST 2013

On 8/22/13 3:25 PM, MUSYOKA THOMMAS wrote:
> Dear users,
> I am dealing with molecular docking of ligands to cysteine proteases and i
> got several questions to pose.
> 1) For example looking at the structure of Falcipain-2 (PDBID=2OUL), i can
> see it got several water molecules. when and how do i determine whether i
> should stripe off the molecules. According to
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html,
> i should check if the the catalytic site has water molecules. How do i
> determine this?

You need to do background reading about the enzyme, its mechanism, and the 
specific structure that you are using.

I removed the waters from lysozyme for that tutorial to avoid confusion that 
would undoubtedly arise from multiple SOL entries after genbox and then the 
choice of group for embedding ions.  In general, one should not necessarily 
dismiss crystal waters.  There's probably never any harm in keeping them.

> 2) I got a cysteine PDB structure and a docked ligand PDB. How do i combine
> the two to make one PDB file that i can use as my starting structure for MD
> simulations?

If you've done docking, you already have it.  The coordinate file is not the 
challenge, the topology is.  Deriving parameters for an arbitrary small molecule 
for an existing parent force field is an advanced topic, one that can require 
weeks or months of work.  You will have to invest considerable time reading 
about the underlying theory of your chosen force field and how one goes about 
deriving new parameters.

As for dealing with the complex itself, there's a tutorial for that:




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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